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1RP7
Asym. Unit
Info
Asym.Unit (272 KB)
Biol.Unit 1 (266 KB)
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(1)
Title
:
E. COLI PYRUVATE DEHYDROGENASE INHIBITOR COMPLEX
Authors
:
P. Arjunan, K. Chandrasekhar, W. Furey
Date
:
03 Dec 03 (Deposition) - 16 Mar 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.09
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Thdp, Thiamin-Thiazolone Diphosphate, Pyruvate Dehydrogenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Arjunan, K. Chandrasekhar, M. Sax, A. Brunskill, N. Nemeria, F. Jordan, W. Furey
Structural Determinants Of Enzyme Binding Affinity: The E1 Component Of Pyruvate Dehydrogenase From Escherichia Coli In Complex With The Inhibitor Thiamin Thiazolone Diphosphate.
Biochemistry V. 43 2405 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TZDa)
2b: 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TZDb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MG
2
Ligand/Ion
MAGNESIUM ION
2
TZD
2
Ligand/Ion
2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYLTRIHYDROGEN DIPHOSPHATE
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP B:230 , ASN B:260 , GLN B:262 , TZD B:887 , HOH B:889
BINDING SITE FOR RESIDUE MG B 888
2
AC2
SOFTWARE
ASP A:230 , ASN A:260 , GLN A:262 , TZD A:889 , HOH A:1113
BINDING SITE FOR RESIDUE MG A 890
3
AC3
SOFTWARE
ASP A:521 , ILE A:569 , GLU A:571 , PHE A:602 , ARG A:606 , HIS A:640 , HOH A:892 , HOH A:893 , SER B:109 , GLN B:140 , HIS B:142 , VAL B:192 , SER B:193 , MET B:194 , GLY B:229 , ASP B:230 , GLY B:231 , GLU B:232 , GLU B:235 , ASN B:260 , GLN B:262 , LYS B:392 , MG B:888 , HOH B:889 , HOH B:890 , HOH B:891
BINDING SITE FOR RESIDUE TZD B 887
4
AC4
SOFTWARE
SER A:109 , GLN A:140 , HIS A:142 , VAL A:192 , SER A:193 , MET A:194 , GLY A:229 , ASP A:230 , GLY A:231 , GLU A:232 , GLU A:235 , ASN A:260 , GLN A:262 , ARG A:263 , LEU A:264 , LYS A:392 , MG A:890 , HOH A:924 , HOH A:1113 , ASP B:521 , GLU B:522 , ILE B:569 , GLU B:571 , PHE B:602 , ARG B:606 , HIS B:640 , HOH B:950
BINDING SITE FOR RESIDUE TZD A 889
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1rp7a2 (A:56-470)
1b: SCOP_d1rp7b2 (B:56-470)
2a: SCOP_d1rp7a1 (A:471-700)
2b: SCOP_d1rp7b1 (B:471-700)
3a: SCOP_d1rp7a3 (A:701-886)
3b: SCOP_d1rp7b3 (B:701-886)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
TK-like PP module
(24)
Protein domain
:
Pyruvate dehydrogenase E1 component, PP module
(8)
Escherichia coli [TaxId: 562]
(8)
1a
d1rp7a2
A:56-470
1b
d1rp7b2
B:56-470
Family
:
TK-like Pyr module
(16)
Protein domain
:
Pyruvate dehydrogenase E1 component, Pyr module
(6)
Escherichia coli [TaxId: 562]
(6)
2a
d1rp7a1
A:471-700
2b
d1rp7b1
B:471-700
Fold
:
TK C-terminal domain-like
(79)
Superfamily
:
TK C-terminal domain-like
(79)
Family
:
Transketolase C-terminal domain-like
(21)
Protein domain
:
Pyruvate dehydrogenase E1 component, C-domain
(8)
Escherichia coli [TaxId: 562]
(8)
3a
d1rp7a3
A:701-886
3b
d1rp7b3
B:701-886
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1rp7A03 (A:706-886)
1b: CATH_1rp7B03 (B:706-886)
2a: CATH_1rp7A02 (A:471-705)
2b: CATH_1rp7B02 (B:471-705)
2c: CATH_1rp7A01 (A:56-470)
2d: CATH_1rp7B01 (B:56-470)
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)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.920, no name defined]
(73)
Escherichia coli, escherichia coli o157:h7. ,. Organism_taxid: 562,83334. Strain: , o157:h7.
(1)
1a
1rp7A03
A:706-886
1b
1rp7B03
B:706-886
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Escherichia coli, escherichia coli o157:h7. ,. Organism_taxid: 562,83334. Strain: , o157:h7.
(1)
2a
1rp7A02
A:471-705
2b
1rp7B02
B:471-705
2c
1rp7A01
A:56-470
2d
1rp7B01
B:56-470
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Transketolase_N_1rp7B01 (B:350-474)
1b: PFAM_Transketolase_N_1rp7B02 (B:350-474)
1c: PFAM_Transketolase_N_1rp7B03 (B:350-474)
1d: PFAM_Transketolase_N_1rp7B04 (B:350-474)
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Clan
:
THDP-binding
(106)
Family
:
Transketolase_N
(22)
Escherichia coli O157:H7
(3)
1a
Transketolase_N-1rp7B01
B:350-474
1b
Transketolase_N-1rp7B02
B:350-474
1c
Transketolase_N-1rp7B03
B:350-474
1d
Transketolase_N-1rp7B04
B:350-474
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Asymmetric Unit 1
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Asym.Unit (272 KB)
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Header - Biol.Unit 1
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